Existing mass spectrometers usually analyze ions from one ion source at a time. Exceptions include the use of ion traps, or when a second ion source is used which is a built-in electron impact ionization source. One way to couple multiple ion sources to a 3D ion trap includes injecting ions from a second ion source through a hole in the ring electrode of the ion trap, as described in Stephenson, J. L and McLuckey, S. A. (1997), Int. J. Mass Spectrom. Ion Processes, 162, pp. 89-106. Another way includes using a turning quadrupole. This method is not limited to 3D ion traps and can be used for various analyzers. For example, in one case, three ion sources were coupled to an ion trap through the turning quadrupole, as described in Badman, E. R.; Chrisman, P. A. and McLuckey, S. A., 2002, Anal. Chem., 74, pp. 6237-6243. However, in the configuration taught by Badman et al., the three ion sources could not simultaneously supply ions to the ion trap. In limited cases, some two-dimensional ion traps (or linear traps) can be used to accept ions from two ion sources and allow the ions sources to operate simultaneously (Coon J. J., Syka, J. E. P., Schwartz, J. C., Shabanowitz, J., and Hunt, D. F., 2004, Int. J. Mass Spectrom., 236, pp. 33-42).
Another approach for a multi-input ion source is described in Krutchinsky, A. N.; Zhang, W. and Chait, B. T., 2000, “Rapidly Switchable MALDI and Electrospray Quadrupole-Time-of-Flight Mass Spectrometry for Protein Identification”, J. Am. Soc. Mass Spectrometry, V. 11, pp. 493-504. Krutchinsky et al. describe a mass spectrometer with rapidly switchable MALDI and electrospray ion sources. However, this instrument requires one of the ion sources to be a MALDI source. Further, the MALDI source must be a specially designed MALDI source. Lastly, the multiple ion sources cannot be used simultaneously with this instrument since the two ion sources are arranged in series rather than in parallel.
Unfortunately, for most existing ion sources, manual interference is required when changing from one ion source to another ion source, such as when changing between an ESI ion source and an oMALDI ion source, for example. The manual interference usually involves venting at least part of the vacuum chamber, resulting in a noticeable pump-down time before the machine is back in operation.